I can try to answer the other questions.
SYS__INDEXES is empty and actually not used at all in the database. We should probably remove it from the database. In the database structure XML files there is a SYS_INDEXES collection that contains the list of the default database table indexes, and the database table was supposed to mirror this, but in the end this was not implemented.
The Tool menu has disappeared from the DbEditor in Efficy 11, the menu no longer fits in the visual design of the form. I'll make a change so that you can still enable it by pressing a key combination (e.g. Ctrl-M).